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metamouse-local.wdl
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metamouse-local.wdl
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version 1.0
import "arraycheck_simple.wdl" as module1
import "arraycheck_rdata.wdl" as module2
import "filechecker.wdl" as module3
import "enumouse.wdl" as module4
import "big_cheese.wdl" as module5
workflow metamouse {
input {
File SB_nullmodel
File SB_pheno
File SB_report
File SB_report_invnorm
File local_nullmodel
File local_pheno
File local_report
File local_report_invnorm
Boolean run_failure_cases = false
}
###################### these tasks should PASS ######################
call module1.stuart_arraycheck_simple as pass_ACS {
input:
test = [local_nullmodel, local_pheno, local_report, local_report_invnorm],
truth = [SB_nullmodel, SB_pheno, SB_report, SB_report_invnorm]
}
call module2.stuart_arraycheck_rdata as pass_ACR {
input:
test = [local_nullmodel, local_pheno, local_report, local_report_invnorm],
truth = [SB_nullmodel, SB_pheno, SB_report, SB_report_invnorm]
}
call module3.stuart_filechecker as pass_FC {
input:
test = SB_pheno,
truth = local_pheno
}
call module4.stuart_enumouse as pass_ENU {
input:
genome_build = "hg38"
}
call module5.stuart_bigcheese {
input:
some_file = local_nullmodel,
some_group_of_files = [SB_nullmodel, SB_pheno, SB_report, SB_report_invnorm]
}
if (run_failure_cases) {
###################### these tasks should FAIL ######################
call module1.stuart_arraycheck_simple as fail_ACS_fastfail {
input:
test = [local_nullmodel, local_pheno, local_report, local_report_invnorm],
truth = [SB_nullmodel, SB_pheno, SB_report, SB_report_invnorm],
fastfail = true
}
call module2.stuart_arraycheck_rdata as fail_ACR_exact {
input:
test = [local_nullmodel, local_pheno, local_report, local_report_invnorm],
truth = [SB_nullmodel, SB_pheno, SB_report, SB_report_invnorm],
exact = true
}
call module2.stuart_arraycheck_rdata as fail_ACR_fastfail {
input:
test = [local_nullmodel, local_pheno, local_report, local_report_invnorm],
truth = [SB_nullmodel, SB_pheno, SB_report, SB_report_invnorm],
tolerance = 0.000000000000000000000000000001,
fastfail = true
}
call module4.stuart_enumouse as fail_ENU {
input:
genome_build = "hg39"
}
call module4.stuart_enumouse as fail_ENU_subset {
input:
genome_build = "38"
}
}
}